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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ), 'gf_id' => 'HOM05D001362', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001362' ), 'data_identifier' => 'HOM05D001362', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001362', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '459', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p41860' => 'bna', 'A02p41890' => 'bna', 'A03p05920' => 'bna', 'A06p07640' => 'bna', 'A06p28680' => 'bna', 'A09p17190' => 'bna', 'A10p24900' => 'bna', 'Aa31LG11G1540' => 'aar', 'Aa31LG2G9700' => 'aar', 'Aa31LG3G14360' => 'aar', 'Aa31LG3G19090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2884' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1240' => 'aag', 'Actinidia02652' => 'ach', 'Actinidia13748' => 'ach', 'Actinidia18309' => 'ach', 'Actinidia20622' => 'ach', 'Actinidia22120' => 'ach', 'Actinidia22121' => 'ach', 'Actinidia30591' => 'ach', 'Actinidia34000' => 'ach', 'Ah.01g013120' => 'amhyb', 'Ah.02g131480' => 'amhyb', 'Ah.03g135580' => 'amhyb', 'Ah.11g046820' => 'amhyb', 'AL1G21810' => 'aly', 'AL2G15660' => 'aly', 'AL6G23920' => 'aly', 'AL8G38740' => 'aly', 'Aqoxy3G04233' => 'aox', 'Aqoxy5G03158' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5ZRL6J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D9KF4I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DE24KT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMIU0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KPY0UD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MPCU6S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SL3LA8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TD68IP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TQKX61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UP9I24' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W3TTRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WVN0A7' => 'arhy', 'AT1G10870' => 'ath', 'AT1G60860' => 'ath', 'AT5G13300' => 'ath', 'AT5G61980' => 'ath', 'ATR0582G329' => 'atr', 'ATR0618G136' => 'atr', 'Atru.chr11.1215' => 'acertr', 'Atru.chr11.1216' => 'acertr', 'Atru.chr12.1404' => 'acertr', 'Atru.chr6.1907' => 'acertr', 'AUR62005710' => 'cqu', 'AUR62009527' => 'cqu', 'AUR62012871' => 'cqu', 'AUR62017641' => 'cqu', 'AUR62028845' => 'cqu', 'AUR62041692' => 'cqu', 'BcaB01g05364' => 'bca', 'BcaB02g09610' => 'bca', 'BcaB07g29806' => 'bca', 'BcaB07g31233' => 'bca', 'BcaC01g02452' => 'bca', 'BcaC04g19124' => 'bca', 'BcaC04g22275' => 'bca', 'BcaC05g24967' => 'bca', 'BcaNung04759' => 'bca', 'BolC2t12236H' => 'bol', 'BolC3t13195H' => 'bol', 'BolC3t18766H' => 'bol', 'BolC5t29663H' => 'bol', 'BolC9t55040H' => 'bol', 'BolC9t59216H' => 'bol', 'BraA02t09123Z' => 'bra', 'BraA03t09930Z' => 'bra', 'BraA06t23966Z' => 'bra', 'BraA06t25808Z' => 'bra', 'BraA09t37352Z' => 'bra', 'BraA10t44553Z' => 'bra', 'C02p61800' => 'bna', 'C03p06790' => 'bna', 'C03p06800' => 'bna', 'C03p06950' => 'bna', 'C03p65120' => 'bna', 'C05p09230' => 'bna', 'C09p21340' => 'bna', 'C09p63770' => 'bna', 'CAN.G16.16' => 'can', 'CAN.G194.8' => 'can', 'CAN.G521.5' => 'can', 'CAN.G843.16' => 'can', 'CANSAT56G1813' => 'cansat', 'CANSAT64G2489' => 'cansat', 'CARHR011090' => 'chi', 'CARHR051880' => 'chi', 'CARHR200140' => 'chi', 'CARHR275780' => 'chi', 'Carub.0001s1041' => 'cru', 'Carub.0001s1042' => 'cru', 'Carub.0002s0446' => 'cru', 'Carub.0006s1147' => 'cru', 'Carub.0008s2267' => 'cru', 'Ca_03048_v3' => 'car', 'Ca_07075_v3' => 'car', 'Ca_10881_v3' => 'car', 'Ca_16810_v3' => 'car', 'CBR_g23110' => 'cbr', 'Cc00_g12240' => 'ccan', 'Cc00_g30370' => 'ccan', 'Cc00_g30380' => 'ccan', 'Cc11_g02240' => 'ccan', 'Cc11_g15080' => 'ccan', 'CDE02G0857' => 'cde', 'CDE04G3493' => 'cde', 'CDE06G1363' => 'cde', 'CDE06G1397' => 'cde', 'CDE06G2303' => 'cde', 'CDE08G0756' => 'cde', 'Cfa009443' => 'cfa', 'Cfa015131' => 'cfa', 'Cfa018714' => 'cfa', 'Cfa027013' => 'cfa', 'Ciclev10004318m.g' => 'ccl', 'Ciclev10030748m.g' => 'ccl', 'Ciclev10030874m.g' => 'ccl', 'CiPaw.05G102000' => 'cil', 'CiPaw.05G164100' => 'cil', 'CiPaw.06G108900' => 'cil', 'ClCG07G006930' => 'cla', 'ClCG07G006950' => 'cla', 'ClCG07G011900' => 'cla', 'COL.COLO4_21780' => 'col', 'COL.COLO4_27644' => 'col', 'COL.COLO4_27645' => 'col', 'COL.COLO4_37244' => 'col', 'Cpa.g.sc13.160' => 'cpa', 'Cpa.g.sc13.161' => 'cpa', 'Cpa.g.sc2.54' => 'cpa', 'Cpa.g.sc2.56' => 'cpa', 'Cpa.g.sc2.57' => 'cpa', 'Cpa.g.sc38.90' => 'cpa', 'Cpa.g.sc38.91' => 'cpa', 'Cre03.g154150' => 'cre', 'CsaV3_4G002260' => 'csa', 'CsaV3_5G015210' => 'csa', 'CSS0009852' => 'camsi', 'CSS0015216' => 'camsi', 'CSS0040545' => 'camsi', 'CSS0040907' => 'camsi', 'CSS0043430' => 'camsi', 'CSS0043909' => 'camsi', 'CSS0045005' => 'camsi', 'CSS0045490' => 'camsi', 'DCAR_021405' => 'dca', 'DCAR_023425' => 'dca', 'DCAR_024630' => 'dca', 'Dinv13730' => 'din', 'Dinv17891' => 'din', 'Dinv19301' => 'din', 'Dinv19303' => 'din', 'Dinv23215' => 'din', 'Dinv34962' => 'din', 'Duzib052G0928' => 'dzi', 'Duzib132G0054' => 'dzi', 'Duzib248G0721' => 'dzi', 'Duzib248G0895' => 'dzi', 'Duzib251G0196' => 'dzi', 'ECA232G3875' => 'eca', 'ECA234G1014' => 'eca', 'ECA246G5117' => 'eca', 'EL10Ac5g11298' => 'bvu', 'EL10Ac6g13605' => 'bvu', 'EL10Ac7g17943' => 'bvu', 'EL10Ac9g22896' => 'bvu', 'Eucgr.G01966' => 'egr', 'Eucgr.J00845' => 'egr', 'FAN07G0751' => 'fan', 'FAN07G1053' => 'fan', 'FAN12G1930' => 'fan', 'FAN12G2947' => 'fan', 'FAN12G3894' => 'fan', 'FAN13G0724' => 'fan', 'FAN17G1682' => 'fan', 'FAN17G1894' => 'fan', 'FAN18G0210' => 'fan', 'FvH4_4g22770' => 'fve', 'FvH4_4g36580' => 'fve', 'FvH4_5g09370' => 'fve', 'Glyma.04G200800' => 'gma', 'Glyma.05G200700' => 'gma', 'Glyma.06G164667' => 'gma', 'Glyma.08G257600' => 'gma', 'Glyma.11G104500' => 'gma', 'Glyma.12G029500' => 'gma', 'Glyma.18G282000' => 'gma', 'Gohir.A01G020900' => 'ghi', 'Gohir.A03G056400' => 'ghi', 'Gohir.A03G111300' => 'ghi', 'Gohir.A03G111400' => 'ghi', 'Gohir.A03G111500' => 'ghi', 'Gohir.A03G151900' => 'ghi', 'Gohir.A12G155000' => 'ghi', 'Gohir.A13G026700' => 'ghi', 'Gohir.D01G019400' => 'ghi', 'Gohir.D02G135900' => 'ghi', 'Gohir.D02G136000' => 'ghi', 'Gohir.D02G136100' => 'ghi', 'Gohir.D02G175100' => 'ghi', 'Gohir.D03G110100' => 'ghi', 'Gohir.D12G158200' => 'ghi', 'Gohir.D13G025500' => 'ghi', 'Gorai.002G021700' => 'gra', 'Gorai.003G116500' => 'gra', 'Gorai.005G151900' => 'gra', 'Gorai.005G152000' => 'gra', 'Gorai.005G152100' => 'gra', 'Gorai.005G196700' => 'gra', 'Gorai.008G171000' => 'gra', 'Gorai.013G028700' => 'gra', 'GSVIVG01001079001' => 'vvi', 'GSVIVG01008640001' => 'vvi', 'GSVIVG01010214001' => 'vvi', 'HanXRQChr06g0175541' => 'han', 'HanXRQChr09g0273901' => 'han', 'HanXRQChr15g0472971' => 'han', 'HanXRQChr16g0499621' => 'han', 'HanXRQChr17g0540671' => 'han', 'Haze_01541' => 'cav', 'Haze_07106' => 'cav', 'Haze_12495' => 'cav', 'Hma1.2p1_0168F.1_g074000' => 'hma', 'Hma1.2p1_0285F.1_g113860' => 'hma', 'HPP92_005945' => 'vpl', 'HPP92_007041' => 'vpl', 'HPP92_007042' => 'vpl', 'Hund02503' => 'sun', 'Hund10046' => 'sun', 'Hund24315' => 'sun', 'Hund25506' => 'sun', 'Lalb_Chr01g0001631' => 'lal', 'Lalb_Chr02g0144721' => 'lal', 'Lalb_Chr03g0024931' => 'lal', 'Lalb_Chr03g0024941' => 'lal', 'Lalb_Chr06g0164711' => 'lal', 'Lalb_Chr08g0237511' => 'lal', 'Lalb_Chr10g0092201' => 'lal', 'Lalb_Chr12g0202471' => 'lal', 'Lalb_Chr23g0272871' => 'lal', 'Lj1g0005489' => 'lja', 'Lj1g0016671' => 'lja', 'Lj3g0017135' => 'lja', 'Lj4g0013823' => 'lja', 'Lj5A87T64' => 'lonja', 'Lj6A837G32' => 'lonja', 'Lj6C723G12' => 'lonja', 'Lj9C486G12' => 'lonja', 'Lsat_1_v5_gn_0_9201' => 'lsa', 'Lsat_1_v5_gn_4_1580' => 'lsa', 'Lsat_1_v5_gn_4_84620' => 'lsa', 'Manes.06G126100' => 'mes', 'Manes.08G101900' => 'mes', 'Manes.09G187500' => 'mes', 'Manes.10G069200' => 'mes', 'Mapoly0014s0145' => 'mpo', 'Mapoly0015s0027' => 'mpo', 'MBI05_g07842_MAGBIO' => 'mbi', 'MBI06_g28667_MAGBIO' => 'mbi', 'MBI07_g07337_MAGBIO' => 'mbi', 'MBI17_g19038_MAGBIO' => 'mbi', 'MBI19_g30281_MAGBIO' => 'mbi', 'MBI19_g30282_MAGBIO' => 'mbi', 'MCO06G268' => 'mco', 'MCO11G449' => 'mco', 'MCO12G065' => 'mco', 'MD06G1131800' => 'mdo', 'MD13G1008500' => 'mdo', 'MD13G1129800' => 'mdo', 'MD14G1148100' => 'mdo', 'MD16G1006300' => 'mdo', 'MD16G1130100' => 'mdo', 'Medtr3g098680' => 'mtr', 'Medtr4g074170' => 'mtr', 'Medtr7g020860' => 'mtr', 'Medtr8g100100' => 'mtr', 'MELO3C017813.2' => 'cme', 'MELO3C018265.2' => 'cme', 'Migut.I00616' => 'egut', 'Migut.K01064' => 'egut', 'Migut.L00615' => 'egut', 'MSTRG.11227' => 'ama', 'MSTRG.459' => 'ama', 'MSTRG.8049' => 'ama', 'MSTRG.8102' => 'ama', 'Nitab4.5_0000049g0130' => 'nta', 'Nitab4.5_0000129g0320' => 'nta', 'Nitab4.5_0000129g0370' => 'nta', 'Nitab4.5_0000663g0210' => 'nta', 'Nitab4.5_0001419g0030' => 'nta', 'Nitab4.5_0002515g0010' => 'nta', 'Nitab4.5_0002584g0040' => 'nta', 'Nitab4.5_0002584g0050' => 'nta', 'Nitab4.5_0003119g0040' => 'nta', 'Nitab4.5_0008892g0010' => 'nta', 'Nn3g16287' => 'nnu', 'Nn4g22146' => 'nnu', 'Nn4g24893' => 'nnu', 'Nn7g36633' => 'nnu', 'Oeu019440.1' => 'oeu', 'Oeu019442.1' => 'oeu', 'Oeu034637.1' => 'oeu', 'Oeu034638.1' => 'oeu', 'Oeu044512.1' => 'oeu', 'Os02g0632500' => 'osa', 'Os08g0537600' => 'osa', 'Os09g0510700' => 'osa', 'Peaxi162Scf00128g01776' => 'pax', 'Peaxi162Scf00314g00540' => 'pax', 'Peaxi162Scf00329g00715' => 'pax', 'Peaxi162Scf01168g00015' => 'pax', 'PGR004G1729' => 'pgr', 'PGR044G0616' => 'pgr', 'PGR119G1475' => 'pgr', 'PGSC0003DMG400002249' => 'stu', 'PGSC0003DMG400003134' => 'stu', 'PGSC0003DMG400005125' => 'stu', 'PGSC0003DMG400014177' => 'stu', 'PGSC0003DMG400026761' => 'stu', 'PGSC0003DMG400029896' => 'stu', 'PGSC0003DMG401014450' => 'stu', 'PGSC0003DMG402014450' => 'stu', 'Phvul.002G282100' => 'pvu', 'Phvul.008G019300' => 'pvu', 'Phvul.009G161700' => 'pvu', 'Phvul.011G032600' => 'pvu', 'Potri.001G066800' => 'ptr', 'Potri.003G163200' => 'ptr', 'Potri.015G105500' => 'ptr', 'Pp3c14_14420' => 'ppa', 'Pp3c1_32260' => 'ppa', 'Pp3c21_6810' => 'ppa', 'Pp3c6_12760' => 'ppa', 'PRCOL_00004515' => 'pco', 'Prupe.1G216500' => 'ppe', 'Prupe.1G344300' => 'ppe', 'Prupe.5G142800' => 'ppe', 'Psat0s236g0240' => 'psa', 'Psat0s5368g0080' => 'psa', 'Psat2g147520' => 'psa', 'Psat3g190200' => 'psa', 'Psat7g039200' => 'psa', 'Psat7g173960' => 'psa', 'PSO017G4969' => 'pso', 'PSO063G1458' => 'pso', 'PSO478G2522' => 'pso', 'PSO782G2670' => 'pso', 'QL03p043127' => 'qlo', 'QL03p049594' => 'qlo', 'QL10p000700' => 'qlo', 'QL10p000736' => 'qlo', 'RcHm_v2.0_Chr4g0428991' => 'rch', 'RcHm_v2.0_Chr4g0446341' => 'rch', 'RcHm_v2.0_Chr7g0188801' => 'rch', 'Rhsim08G0196400' => 'rsi', 'Rhsim09G0077700' => 'rsi', 'Rhsim12G0017800' => 'rsi', 'Sabra01G0046400' => 'sbr', 'Sabra03G0118700' => 'sbr', 'Sabra15G0125800' => 'sbr', 'SalBow2G3327' => 'sbo', 'SalBow7G0758' => 'sbo', 'Sc04g0000220' => 'sci', 'Sc04g0010530' => 'sci', 'Sc06g0005820' => 'sci', 'Sc11g0000130' => 'sci', 'Sed0010535' => 'sed', 'Sed0010766' => 'sed', 'Sed0023780' => 'sed', 'SEGI_04163' => 'sgi', 'SEGI_15104' => 'sgi', 'SEGI_15577' => 'sgi', 'SEGI_25141' => 'sgi', 'SEGI_25894' => 'sgi', 'SEGI_34227' => 'sgi', 'SEGI_38345' => 'sgi', 'SEGI_38375' => 'sgi', 'SEGI_41210' => 'sgi', 'SGA_v2.0_scaffold258G45788' => 'sas', 'SGA_v2.0_scaffold40G15624' => 'sas', 'SGA_v2.0_scaffold86G26851' => 'sas', 'SGA_v2.0_scaffold98G29276' => 'sas', 'SHI04126' => 'shi', 'SMO143G0171' => 'smo', 'SMO246G0023' => 'smo', 'Solyc03g118260.3' => 'sly', 'Solyc04g008660.4' => 'sly', 'Solyc05g023750.3' => 'sly', 'Solyc12g042170.3' => 'sly', 'Solyc12g042180.1' => 'sly', 'Sopen03g037170' => 'spe', 'Sopen04g003830' => 'spe', 'Sopen05g018360' => 'spe', 'Sopen12g021210' => 'spe', 'Sp1g09570' => 'spa', 'Sp2g03810' => 'spa', 'Sp2g25160' => 'spa', 'Sp6g30690' => 'spa', 'TAR622G0719' => 'tar', 'TAR629G2226' => 'tar', 'TAR629G3420' => 'tar', 'THA.LOC104801806' => 'tha', 'THA.LOC104807322' => 'tha', 'THA.LOC104809594' => 'tha', 'THA.LOC104819423' => 'tha', 'THA.LOC104825279' => 'tha', 'Thecc.02G193400' => 'tca', 'Thecc.02G309900' => 'tca', 'Thecc.03G139300' => 'tca', 'Thhalv10003653m.g' => 'esa', 'Thhalv10006873m.g' => 'esa', 'Thhalv10012699m.g' => 'esa', 'Thhalv10023294m.g' => 'esa', 'TPR.G12802' => 'tpr', 'TPR.G21553' => 'tpr', 'TPR.G21588' => 'tpr', 'TPR.G4572' => 'tpr', 'TWI23G0713' => 'twi', 'TWI36G0034' => 'twi', 'TWI74G1056' => 'twi', 'TWI75G1144' => 'twi', 'unitig_0.g1088' => 'ugi', 'unitig_0.g1089' => 'ugi', 'unitig_22.g6380' => 'ugi', 'unitig_8.g3107' => 'ugi', 'unitig_8.g3118' => 'ugi', 'vmacro01024' => 'vma', 'vmacro10793' => 'vma', 'vmacro10794' => 'vma', 'vmacro19176' => 'vma', 'VMungo0251G2767' => 'vmu', 'VMungo1127G1377' => 'vmu', 'VMungo1309G2131' => 'vmu', 'VMungo1309G3088' => 'vmu', 'VMungo1383G1921' => 'vmu', 'Zm00001eb035160' => 'zma', 'Zm00001eb037010' => 'zma', 'Zm00001eb047350' => 'zma', 'Zm00001eb087360' => 'zma', 'Zm00001eb129670' => 'zma', 'Zm00001eb173800' => 'zma', 'Zm00001eb175550' => 'zma', 'Zm00001eb185350' => 'zma', 'Zm00001eb185370' => 'zma', 'Zm00001eb232350' => 'zma', 'Zm00001eb237250' => 'zma', 'Zm00001eb259830' => 'zma', 'Zm00001eb318030' => 'zma', 'Zm00001eb341950' => 'zma', 'Zm00001eb411280' => 'zma' ) $gf_id = 'HOM05D001362' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001362' ) $data_identifier = 'HOM05D001362' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 8, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 9, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 15 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411280' $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